Contacts of the helix formed by residues 617 - 625 (chain B) in PDB entry 6T2C
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 617 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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583B THR* 3.3 20.5 - - - +
584B ILE* 3.3 17.3 + - - +
585B SER* 3.1 39.6 + - - +
588B GLY* 5.8 0.2 - - - -
589B LEU* 5.4 0.5 - - - +
615B LEU 3.6 1.6 + - - -
616B MET* 1.3 73.1 - - - +
618B PRO* 1.3 73.7 - - + +
619B ASP* 3.2 13.2 - - - +
620B TYR* 3.0 22.3 + - - +
621B ARG* 3.2 8.8 + - - +
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Residues in contact with PRO 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616B MET 4.2 1.1 - - - +
617B ASP* 1.3 86.3 - - + +
619B ASP* 1.3 59.2 + - - +
621B ARG* 3.8 32.1 - - - +
622B GLY* 2.9 25.3 + - - -
105C VAL* 4.6 3.4 - - - +
108C VAL* 5.5 0.9 - - - +
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Residues in contact with ASP 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B THR* 5.5 4.8 - - - +
617B ASP* 3.4 23.1 - - - +
618B PRO* 1.3 72.1 - - - +
620B TYR* 1.3 61.0 + - - +
622B GLY* 3.5 0.9 + - - -
623B ARG* 2.9 56.9 + - - +
105C VAL* 4.3 13.6 - - + +
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Residues in contact with TYR 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B LEU* 4.2 13.5 - - + -
583B THR* 4.2 11.4 - - + -
588B GLY 3.9 0.7 - - - -
589B LEU* 3.7 38.6 - - + -
590B LEU* 3.3 20.9 + - - +
593B ASP* 2.3 39.3 + - - +
616B MET* 3.6 35.7 - - + -
617B ASP* 3.0 20.0 + - - +
619B ASP* 1.3 82.0 + - - +
621B ARG* 1.3 55.7 - - - +
623B ARG* 3.3 7.3 + - - +
624B LEU* 2.9 37.9 + - + +
100C ASN* 4.0 19.9 - - - +
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Residues in contact with ARG 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613B TRP* 3.1 75.6 + - + +
614B SER* 5.3 1.2 - - - +
616B MET* 4.0 32.9 + - + -
617B ASP 3.2 7.9 + - - +
618B PRO* 3.8 37.0 + - - +
620B TYR* 1.3 79.9 - - - +
622B GLY* 1.3 61.1 + - - +
624B LEU* 3.1 4.7 + - - +
625B CYS* 3.1 26.6 + - - +
108C VAL* 3.8 19.5 + - + +
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Residues in contact with GLY 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618B PRO 2.9 18.5 + - - -
619B ASP 3.8 1.1 - - - -
621B ARG* 1.3 78.5 - - - +
623B ARG* 1.3 61.8 + - - +
624B LEU 3.4 0.2 + - - -
625B CYS 4.3 0.2 - - - -
626B ASN* 3.7 18.2 + - - +
105C VAL* 4.3 3.1 - - - -
106C SER* 3.7 31.3 + - - -
108C VAL* 3.8 17.2 - - - +
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Residues in contact with ARG 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619B ASP* 2.9 50.0 + - - +
620B TYR* 3.7 5.6 - - - +
621B ARG 3.3 0.2 - - - -
622B GLY* 1.3 76.6 - - - +
624B LEU* 1.3 60.7 + - - +
626B ASN* 4.3 1.6 + - - +
99C TRP* 3.4 32.9 + - - +
100C ASN* 3.6 24.4 - - - +
101C ARG 3.5 16.3 + - - -
102C ALA* 4.4 4.9 - - - +
103C GLY 3.0 42.7 + - - +
104C PRO 4.6 5.8 - - - -
105C VAL* 3.7 20.9 - - + +
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Residues in contact with LEU 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590B LEU* 3.9 20.6 - - + -
609B VAL* 5.1 1.6 - - + -
616B MET* 4.1 14.6 - - + -
620B TYR* 2.9 36.8 + - + +
621B ARG* 3.1 9.8 + - - +
623B ARG* 1.3 77.1 - - - +
625B CYS* 1.3 65.5 + - - +
626B ASN 3.2 6.3 + - - +
662B THR* 3.8 28.0 - - + -
663B THR* 3.3 39.3 + - - +
664B HIS* 4.1 7.9 - - + -
100C ASN* 3.4 28.9 - - - +
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Residues in contact with CYS 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B VAL* 4.6 7.0 - - - -
613B TRP* 4.4 22.4 - - - -
616B MET* 6.1 0.4 - - - -
621B ARG* 3.1 14.3 + - - +
622B GLY 4.3 0.7 - - - -
624B LEU* 1.3 77.8 - - - +
626B ASN* 1.3 64.1 + - - +
627B PRO* 3.5 6.2 - - - +
661B ALA 4.8 3.1 - - - +
662B THR* 3.7 26.0 - - + +
108C VAL* 3.5 30.4 - - + +
111C TYR* 3.7 32.6 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il